ararpy 0.1.11__py3-none-any.whl → 0.1.13__py3-none-any.whl

ararpy/smp/diffusion_funcs.py

@@ -14,28 +14,29 @@
 
 import os
 import shutil
-import string
-
 import numpy as np
-from .sample import Sample
-import ararpy as ap
-import matplotlib as mpl
-import scipy.stats as stats
+np.set_printoptions(precision=18, threshold=10000, linewidth=np.inf)
 import math
+import random
+import scipy.stats as stats
+from scipy.interpolate import griddata
 from scipy.special import comb
 from datetime import datetime as dt
 import re
 import time
 import ctypes
 import gc
-import random
-
+import matplotlib as mpl
 mpl.use('TkAgg')
 import matplotlib.pyplot as plt
 
-np.set_printoptions(precision=18, threshold=10000, linewidth=np.inf)
+from .sample import Sample
+from .. import calc
+# import ararpy as ap
 
 
+import numpy as np
+
 def is_number(s):
     try:
         float(s)
@@ -167,7 +168,7 @@ class DiffArrmultiFunc(DiffSample):
         print(f"{self.telab = }")
         print(f"{self.tilab = }")
 
-    def main(self):
+    def main(self, **params):
 
         print(f"\n======================================")
         print(f"Run Arrmulti Main | ")
@@ -286,7 +287,7 @@ class DiffArrmultiFunc(DiffSample):
                 amax = 0.
                 mct = 0
                 chisq = 1.0e30
-
+                print(f"{mct = } > 30, continue!!!")
                 continue
 
             nc = 0
@@ -1436,7 +1437,7 @@ class DiffArrmultiFunc(DiffSample):
         return xran, yran
 
     def arr(self, e, ord, dzx, fmod, f, telab, tilab, xlogd,
-            ns=200, r=1.987e-3, pi=3.141592654, ee=0.4342944879, acut=0, b=1, imp=1):
+            ns=200, r=1.987e-3, pi=3.141592654, ee=0.4342944879, acut=0.5, b=8, imp=2):
 
         # print(f"{e = }")
         # print(f"{ord = }")
@@ -3321,11 +3322,11 @@ class DiffDraw(DiffSample):
 
     def get_plot_data(self):
 
-        k1 = [x, y1, y2] = ap.calc.spectra.get_data(self.age, self.sage, [i * 100 for i in self.f], cumulative=True)
+        k1 = [x, y1, y2] = calc.spectra.get_data(self.age, self.sage, [i * 100 for i in self.f], cumulative=True)
         k2 = []
         k3 = []
         for cyc in range(self.mcyc):
-            x, y1, y2 = ap.calc.spectra.get_data(
+            x, y1, y2 = calc.spectra.get_data(
                 self.mage[cyc, :], np.zeros(self.mage[cyc, :].size), self.mf[cyc, :], cumulative=True)
             k2.append([x, y1, y2])
             k3.append([self.mcage[cyc, :], self.mcte[cyc, :]])
@@ -3355,7 +3356,7 @@ class DiffDraw(DiffSample):
         axs.plot(data[0][0], data[0][1], c='blue')
 
         for cyc in range(self.mcyc):
-            # x, y1, y2 = ap.calc.spectra.get_data(self.mage[cyc, :], np.zeros(self.mage[cyc, :].size), self.mf[cyc, :],
+            # x, y1, y2 = calc.spectra.get_data(self.mage[cyc, :], np.zeros(self.mage[cyc, :].size), self.mf[cyc, :],
             #                                      cumulative=True)
             axs.plot(data[1][cyc][0], data[1][cyc][2], c='red')
             axs.plot(data[1][cyc][0], data[1][cyc][1], c='red')
@@ -3501,25 +3502,25 @@ class InsideTemperatureCalibration:
                 file_out.writelines(f"{seq.SP = }, {seq.MaxTime = }, conf MaxTime = {max(x_conf)} \n")
                 file2_out.writelines(f"SP = {seq.SP}, MaxTime = {max(x_conf)} \n")
 
-                beta = ap.calc.regression.polynomial(y1_conf, x_conf, degree=degree)[5]
+                beta = calc.regression.polynomial(y1_conf, x_conf, degree=degree)[5]
                 ax.plot(x_conf, np.sum(beta * np.array([x_conf ** i for i in range(degree + 1)]).transpose(), axis=1),
                         c='blue')
                 file_out.writelines("BetaY1\t" + "\t".join([str(i) for i in beta]) + "\n")
                 file2_out.writelines("\t".join([str(i) for i in beta]) + "\n")
 
-                beta = ap.calc.regression.polynomial(y2_conf, x_conf, degree=degree)[5]
+                beta = calc.regression.polynomial(y2_conf, x_conf, degree=degree)[5]
                 ax.plot(x_conf, np.sum(beta * np.array([x_conf ** i for i in range(degree + 1)]).transpose(), axis=1),
                         c='blue')
                 file_out.writelines("BetaY2\t" + "\t".join([str(i) for i in beta]) + "\n")
-                file2_out.writelines("\t".join([str(i) for i in beta]) + "\n")
+                file2_out.writelines("\t".join([str(i) for fi in beta]) + "\n")
 
-                beta = ap.calc.regression.polynomial(y3_conf, x_conf, degree=degree)[5]
+                beta = calc.regression.polynomial(y3_conf, x_conf, degree=degree)[5]
                 ax.plot(x_conf, np.sum(beta * np.array([x_conf ** i for i in range(degree + 1)]).transpose(), axis=1),
                         c='blue')
                 file_out.writelines("BetaY3\t" + "\t".join([str(i) for i in beta]) + "\n")
                 file2_out.writelines("\t".join([str(i) for i in beta]) + "\n")
 
-                beta = ap.calc.regression.polynomial(y4_conf, x_conf, degree=degree)[5]
+                beta = calc.regression.polynomial(y4_conf, x_conf, degree=degree)[5]
                 ax.plot(x_conf, np.sum(beta * np.array([x_conf ** i for i in range(degree + 1)]).transpose(), axis=1),
                         c='blue')
                 file_out.writelines("BetaY4\t" + "\t".join([str(i) for i in beta]) + "\n")
@@ -3677,13 +3678,10 @@ class InsideTemperatureCalibration:
 
 
 class SmpTemperatureCalibration:
-    def __init__(self, arr_path="", helix_log_path="", libano_log_path=None,
+    def __init__(self, helix_log_path="", libano_log_path=None,
                  name="smp_example", loc=r'D:\DjangoProjects\webarar\static\settings'):
 
         self.name = name
-        self.smp = ap.from_arr(file_path=arr_path)
-        if isinstance(self.smp, Sample):
-            self.name = self.smp.name()
 
         self.loc = loc
 
@@ -3779,7 +3777,8 @@ class SmpTemperatureCalibration:
                     continue
 
                 dt_str, helix, system, service, scripting, userinfo, message1, message2 = line.split("|")
-                dt_utc = dt_str[:26] + dt_str[27:]
+                # dt_str likes 2024-10-23T19:58:59.6662140+02:00, it is too long for datetime parser
+                dt_utc = dt_str[:26] + dt_str[27:]  # dt_utc will be like 2024-10-23T19:58:59.666214+02:00
                 dt_utc = dt.fromisoformat(str(dt_utc)).timestamp()
 
                 if not (self.start_time <= dt_utc <= self.end_time):
@@ -3858,27 +3857,28 @@ class SmpTemperatureCalibration:
 
         file_out.close()
 
+        np.savetxt(os.path.join(self.loc, f"{self.name}-temp.txt"), libano_log, delimiter=',')
+        heating_out = open(os.path.join(self.loc, f"{self.name}-heated-index.txt"), "w")
+        heating_out.writelines([f'{min(i)},{max(i)}\n' for i in yellow_data_index])
+        heating_out.close()
 
-        fig, ax = plt.subplots()
-        fig.set_size_inches(w=12, h=10)
+        plt_plot = False
+        if plt_plot:
 
-        ax.plot(libano_log[0], libano_log[1], c='green')
-        ax.plot(libano_log[0], libano_log[2], c='blue')
-        ax.plot(libano_log[0], libano_log[4], c='red')
-        ax.plot(libano_log[0], libano_log[5], c='red')
-        for i in range(nstep):
-            _index = yellow_data_index[i]
-            ax.plot(libano_log[0, _index], libano_log[4, _index], c='yellow')
-            ax.plot(libano_log[0, _index], libano_log[5, _index], c='yellow')
+            fig, ax = plt.subplots()
+            fig.set_size_inches(w=12, h=10)
 
-        fig.tight_layout()
-        plt.show()
+            ax.plot(libano_log[0], libano_log[1], c='green')
+            ax.plot(libano_log[0], libano_log[2], c='blue')
+            ax.plot(libano_log[0], libano_log[4], c='red')
+            ax.plot(libano_log[0], libano_log[5], c='red')
+            for i in range(nstep):
+                _index = yellow_data_index[i]
+                ax.plot(libano_log[0, _index], libano_log[4, _index], c='yellow')
+                ax.plot(libano_log[0, _index], libano_log[5, _index], c='yellow')
 
-
-        np.savetxt(os.path.join(self.loc, f"{self.name}-temp.txt"), libano_log, delimiter=',')
-        heating_out = open(os.path.join(self.loc, f"{self.name}-heated-index.txt"), "w")
-        heating_out.writelines([','.join([str(j) for j in i]) for i in yellow_data_index])
-        heating_out.close()
+            fig.tight_layout()
+            plt.show()
 
 
         #
@@ -4119,7 +4119,7 @@ class Ran1Generator:
 
         self.count += 1
 
-        print(f"{ran1 = }, {self.count = }")
+        # print(f"{ran1 = }, {self.count = }")
 
         return ran1
 
@@ -4445,19 +4445,15 @@ def kahan_sum(input):
     return sum
 
 
-def get_random_index(length: int = 7):
-    return ''.join(random.choices(string.digits, k=length))
-
-
-def get_random_dir(path: str, length=7, random_index = ""):
+def get_random_dir(path: str, length=7, random_index=""):
     try:
+        exist_ok = random_index != ""
         if random_index == "":
-            random_index = get_random_index(length=length)
+            random_index = calc.basic.get_random_digits(length=length)
         destination_folder = os.path.join(path, random_index)
-        os.makedirs(destination_folder, exist_ok=False)
+        os.makedirs(destination_folder, exist_ok=exist_ok)
         return destination_folder, random_index
     except FileExistsError:
-        random_index = ""
         return get_random_dir(path=path, length=length)
 
 
@@ -4475,7 +4471,7 @@ def run_agemon_dll(sample: Sample, source_dll_path: str, loc: str, data, max_age
     agemon.ni = len(data)
     agemon.nit = agemon.ni
     agemon.max_plateau_age = max_age
-    data = ap.calc.arr.transpose(data)
+    data = calc.arr.transpose(data)
     agemon.telab = [i + 273.15 for i in data[3]]
     agemon.tilab = [i / 5.256E+11 for i in data[4]]  # 1 Ma = 525600000000 minutes
     for i in range(agemon.nit):
@@ -4557,9 +4553,12 @@ def run_agemon_dll(sample: Sample, source_dll_path: str, loc: str, data, max_age
     return
 
 
-def dr2_popov(f, ti):
+def dr2_popov(f, ti, ar, sar, ln=True):
     """
 
+    Used in Popov 2020. It is related to the sphere model.
+    The calculation of Dr2 is from sphere model. Errors are carefully propagated.
+
     Parameters
     ----------
     f: cumulative 39Ar released, array
@@ -4575,97 +4574,201 @@ def dr2_popov(f, ti):
     # =IF(M5<85,(    2/PI()^2*( SQRT(PI()^2-(PI()^3)*M4/100/3)-SQRT(PI()^2-(PI()^3)*M5/100/3)) +M4/100/3-M5/100/3 )/D5/60,     LN((1-M4/100)/(1-M5/100))/PI()^2/D5/60)
 
     f = np.array(f)
-    ti = np.array(ti)
+    ti = np.array(ti)  # in minute
+    ar = np.array(ar)
+    sar = np.array(sar)
+    sar2 = sar ** 2
     n = min(len(f), len(ti))
     ti = ti * 60  # in seconds
+    sti = [0.5 * 60 for i in range(n)]
     pi = math.pi
-    pi = 3.141592654
+    # pi = 3.141592654
     dr2 = np.zeros(n)
 
-    if f[-1] >= 1:
-        f[-1] = 0.99999999
-
-    # Popov 2020
-    a, b = 0, 0
-    for i in range(len(f)):
+    f = np.where(f >= 1, 0.9999999999999999, f)
+    sf = [math.sqrt((sum(ar[i+1:]) / sum(ar) ** 2) ** 2 * sum(sar[:i+1] ** 2) + (sum(ar[:i+1]) / sum(ar) ** 2) ** 2 * sum(sar[i+1:] ** 2)) for i in range(n)]
+
+    # Popov 2020, sphere model
+    model = geometric_model(geo='sphere')
+    dtr2 = [model(bp=0.85)[1](fi) for fi in f]
+    dr2 = [(dtr2[i] - (dtr2[i - 1] if i > 0 else 0)) / ti[i] for i in range(len(dtr2))]
+    dr2[-1] = math.log((1 - f[-2]) / (1 - f[-1])) / pi ** 2 / ti[-1]
+
+    # =IF(M5<85,((-SUM(H5:$H$35)/3/SUM($H$4:$H$35)^2/SQRT(1-PI()/3*SUM($H$4:H4)/SUM($H$4:$H$35))/(D5*60)+SUM(H6:$H$35)/3/SUM($H$4:$H$35)^2/SQRT(1-PI()/3*SUM($H$4:H5)/SUM($H$4:$H$35))/(D5*60)+H5/3/SUM($H$4:$H$35)^2/(D5*60))^2),0)
+    sar_lt = np.zeros(n)  # 偏导数
+    sar_eq = np.zeros(n)  # 偏导数
+    sar_gt = np.zeros(n)  # 偏导数
+    st = np.zeros(n)  # 偏导数
+    sdr2 = np.zeros(n)
+    for i in range(n):
         if i == 0:
-            if f[i] < 85:
-                a = 2 / pi ** 2 * math.sqrt(pi ** 2 - (pi ** 3) * f[i] / 3) + f[i] / 3
-                dr2[i] = ((-6 / (pi ** 1.5) + math.sqrt(36 / pi ** 3 - 4 * f[i] * 3 / pi ** 2)) / (
-                            -6 / pi ** 2)) ** 2 / pi ** 2 / ti[i]
+            if f[i] < 0.85:
+                sar_lt[i] = 0
+                sar_eq[i] = ((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * ((sum(ar) - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
+                sar_gt[i] = ((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * ((0 - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
             else:
-                a = 1 - f[i]
-                dr2[i] = (math.log((f[i] - 1) / (-6 / pi ** 2)) / pi ** 2) / ti[i]
+                sar_lt[i] = 0
+                sar_eq[i] = (1 / (pi ** 2 * ti[i] * (f[i] - 1))) * ((sum(ar) - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
+                sar_gt[i] = (1 / (pi ** 2 * ti[i] * (f[i] - 1))) * ((0 - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
         else:
-            if f[i] < 85:
-                a = 2 / pi ** 2 * math.sqrt(pi ** 2 - (pi ** 3) * f[i] / 3) + f[i] / 3
-                dr2[i] = (b - a) / ti[i]
+            if f[i] < 0.85:
+                sar_lt[i] = ((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * ((sum(ar) - ar[i] - sum(ar[:i])) / sum(ar) ** 2) - ((1 / math.sqrt(1 - pi * f[i-1] / 3) - 1) / (3 * ti[i])) * ((sum(ar) - ar[i-1] - sum(ar[:i-1])) / sum(ar) ** 2)
+                sar_eq[i] = ((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * ((sum(ar) - ar[i] - sum(ar[:i])) / sum(ar) ** 2) - ((1 / math.sqrt(1 - pi * f[i-1] / 3) - 1) / (3 * ti[i])) * ((0 - ar[i-1] - sum(ar[:i-1])) / sum(ar) ** 2)
+                sar_gt[i] = ((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * ((0 - ar[i] - sum(ar[:i])) / sum(ar) ** 2) - ((1 / math.sqrt(1 - pi * f[i-1] / 3) - 1) / (3 * ti[i])) * ((0 - ar[i-1] - sum(ar[:i-1])) / sum(ar) ** 2)
             else:
-                dr2[i] = math.log((1 - f[i - 1]) / (1 - f[i])) / pi ** 2 / ti[i]
-        b = a
+                sar_lt[i] = (1 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (0 - 0)
+                sar_eq[i] = (1 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (sum(ar[i+1:]) - 0)
+                sar_gt[i] = (1 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (sum(ar[i+1:]) - sum(ar[i:]))
+        st[i] = - dr2[i] / ti[i]
+        sdr2[i] = math.sqrt(sar_lt[i] ** 2 * sum(sar2[:i]) + sar_eq[i] ** 2 * sar2[i] + sar_gt[i] ** 2 * sum(sar2[i+1:]) + st[i] ** 2 * sti[i] ** 2)
 
-    print(f"popov {dr2 = }")
+    logdr2 = np.log(dr2) if ln else np.log10(dr2)
+    wt = np.abs(sdr2 / dr2) if ln else np.abs(sdr2 / dr2) / np.log(10)
 
-    return dr2, np.log(dr2)
+    return dtr2, logdr2, wt
 
 
-def dr2_lovera(f, ti, ar, sar):
+def dr2_lovera(f, ti, ar, sar, ln=True):
+    """
+
+    Plane sheet model
+
+    Parameters
+    ----------
+    f
+    ti
+    ar
+    sar
+    ln
+
+    Returns
+    -------
+
+    """
     # Lovera
     f = np.array(f)
     ti = np.array(ti)
+    n = min(len(f), len(ti))
     ar = np.array(ar)
     sar = np.array(sar)
+    sar2 = sar ** 2
     ti = ti * 60  # in seconds
+    sti = [90 for i in range(n)]
     pi = math.pi
     pi = 3.141592654
 
     # sf = sqrt(b ** 2 * siga ** 2 + a ** 2 * sigb ** 2) / (a + b) ** 2
-    sf = [math.sqrt(sar[i + 1:].sum() ** 2 * (sar[:i + 1] ** 2).sum() + ar[:i + 1].sum() ** 2 * (sar[i + 1:] ** 2).sum()) / ar.sum() ** 2 for i in range(len(ar) - 1)]
-    sf.append(0)
+    # sf = [math.sqrt(sar[i + 1:].sum() ** 2 * (sar[:i + 1] ** 2).sum() + ar[:i + 1].sum() ** 2 * (sar[i + 1:] ** 2).sum()) / ar.sum() ** 2 for i in range(len(ar) - 1)]
+    # sf.append(0)
 
     f = np.where(f >= 1, 0.9999999999999999, f)
 
-    imp = 2
-    # imp = 1
-    dtr2 = [pi * (fi / 4) ** 2 if fi <= 0.5 else math.log((1 - fi) * pi ** 2 / 8) / (- pi ** 2) for fi in f]
-    dr2 = [(dtr2[i] - (dtr2[i - 1] if i > 0 else 0)) / ti[i] * imp ** 2 for i in range(len(dtr2))]
-    xlogd = [np.log10(i) for i in dr2]
+    model = geometric_model(geo='plane')
+    dtr2 = [model(bp=0.5)[1](fi) for fi in f]
+    dtr2_1 = [model(bp=0)[1](fi) for fi in f]
+    dtr2_2 = [model(bp=2)[1](fi) for fi in f]
+    dtr2_1.insert(0, 0); dtr2_2.insert(0, 0)
+    # dr2 = [(dtr2[i] - (dtr2[i - 1] if i > 0 else 0)) / ti[i] for i in range(len(dtr2))]
+    dr2 = [((dtr2_1[i+1] - dtr2_1[i]) / ti[i]) if f[i] > 0.5 else ((dtr2_2[i+1] - dtr2_2[i]) / ti[i]) for i in range(len(f))]
+
+    # imp = 2
+    # # imp = 1
+    # dtr2 = [pi * (fi / 4) ** 2 if fi <= 0.5 else math.log((1 - fi) * pi ** 2 / 8) / (- pi ** 2) for fi in f]
+    # dr2 = [(dtr2[i] - (dtr2[i - 1] if i > 0 else 0)) / ti[i] * imp ** 2 for i in range(len(dtr2))]
+    # xlogd = [np.log10(i) for i in dr2]
+
+    sar_lt = np.zeros(n)  # 偏导数
+    sar_eq = np.zeros(n)  # 偏导数
+    sar_gt = np.zeros(n)  # 偏导数
+    st = np.zeros(n)  # 偏导数
+    sdr2 = np.zeros(n)
+    for i in range(n):
+        if i == 0:
+            if f[i] <= 0.5:
+                sar_lt[i] = 0
+                sar_eq[i] = pi / (4 * ti[i]) * ((sum(ar[:i+1]) * 2 - 0) * sum(ar) ** 2 - (sum(ar[:i+1]) ** 2 - sum(ar[:i]) ** 2) * 2 * sum(ar)) / (sum(ar) ** 4)
+                sar_gt[i] = pi / (4 * ti[i]) * ((0 - 0) * sum(ar) ** 2 - (sum(ar[:i+1]) ** 2 - sum(ar[:i]) ** 2) * 2 * sum(ar)) / (sum(ar) ** 4)
+            else:
+                sar_lt[i] = 0
+                sar_eq[i] = (4 / (pi ** 2 * ti[i] * (f[i] - 1))) * ((sum(ar) - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
+                sar_gt[i] = (4 / (pi ** 2 * ti[i] * (f[i] - 1))) * ((0 - ar[i] - sum(ar[:i])) / sum(ar) ** 2)
+        else:
+            if f[i] <= 0.5:
+                sar_lt[i] = pi / (4 * ti[i]) * ((sum(ar[:i+1]) * 2 - sum(ar[:i]) * 2) * sum(ar) ** 2 - (sum(ar[:i+1]) ** 2 - sum(ar[:i]) ** 2) * 2 * sum(ar)) / (sum(ar) ** 4)
+                sar_eq[i] = pi / (4 * ti[i]) * ((sum(ar[:i+1]) * 2 - 0) * sum(ar) ** 2 - (sum(ar[:i+1]) ** 2 - sum(ar[:i]) ** 2) * 2 * sum(ar)) / (sum(ar) ** 4)
+                sar_gt[i] = pi / (4 * ti[i]) * ((0 - 0) * sum(ar) ** 2 - (sum(ar[:i+1]) ** 2 - sum(ar[:i]) ** 2) * 2 * sum(ar)) / (sum(ar) ** 4)
+            else:
+                sar_lt[i] = (4 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (0 - 0)
+                sar_eq[i] = (4 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (sum(ar[i+1:]) - 0)
+                sar_gt[i] = (4 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * (sum(ar[i+1:]) - sum(ar[i:]))
+                if i == n - 1:
+                    sar_lt[i] = 0
+                    sar_eq[i] = 0
+                    sar_gt[i] = 0
+        st[i] = - dr2[i] / ti[i]
+        sdr2[i] = math.sqrt(sar_lt[i] ** 2 * sum(sar2[:i]) + sar_eq[i] ** 2 * sar2[i] + sar_gt[i] ** 2 * sum(sar2[i+1:]) + st[i] ** 2 * sti[i] ** 2)
+
+    # wt = np.abs(sdr2 / dr2)
+    # wt = errcal(f, ti, ar, sar)
+
+    xlogd = logdr2 = np.log(dr2) if ln else np.log10(dr2)
+    #ee = 1 / np.log(10)
+    ee = 0.4342944819
+    wt = np.abs(sdr2 / dr2) if ln else np.abs(sdr2 / dr2) * ee
+    #
+    # print(f"{wt = }")
+    # wt = errcal(f, ti, ar, sar)
+    # print(f"{wt = }")
 
-    wt = errcal(f, ti, a39=ar, sig39=sar)
+    """
+    ### errcal(f, ti, ar, sar)和这里的计算有非常少的差异，但这样的差异足以导致迭代次数变化，但不一定导致agemon结果有大的差异
+    """
 
     return dr2, xlogd, wt
 
 
-def dr2_yang(f, ti):
+def dr2_yang(f, ti, ar, sar, ln=True):
+    """
+
+    Parameters
+    ----------
+    f:
+    ti
+
+    Returns
+    -------
+
+    """
     f = np.array(f)
     ti = np.array(ti)
+    ar = np.array(ar)
+    sar = np.array(sar)
+    sar2 = sar ** 2
     n = min(len(f), len(ti))
     ti = ti * 60  # in seconds
+    sti = [5 for i in range(n)]
     pi = math.pi
     pi = 3.141592654
-    dr2 = np.zeros(n)
-
-    if f[-1] >= 1:
-        f[-1] = 0.99999999
-
-    def _dr2(_fi):
-        if _fi <= 0.85:
-            return (1 - math.sqrt(1 - pi * _fi / 3)) ** 2 / pi
-        else:
-            return math.log((1 - _fi) / (6 / pi ** 2)) / - (pi ** 2)
+    ee = 0.4342944819
 
-    for i in range(len(f)):
-        if i == 0:
-            dr2[i] = _dr2(f[i]) / ti[i]
-        else:
-            dr2[i] = _dr2((f[i] - f[i - 1]) / (1 - f[i - 1])) / ti[i]
+    f = np.array([ar[i] / sum(ar[i:]) for i in range(n)])
+    sf = [math.sqrt(sar[i] ** 2 * sum(ar[i+1:]) ** 2 / sum(ar[i:]) ** 4 + sum(sar[i+1:] ** 2) * ar[i] ** 2 / sum(ar[i:]) ** 4) for i in range(n)]
+    f = np.where(f >= 1, 0.9999999999999999, f)
+    # # print(f"{f = }")
+    # f = [(f[i] - (f[i-1] if i > 0 else 0)) / (1 - (f[i-1] if i > 0 else 0)) for i in range(n)]
 
-    print(f"yang {dr2 = }")
+    model = geometric_model(geo='sphere')
+    dtr2 = np.array([model(bp=0.85)[1](fi) for fi in f])
+    sdtr2 = [abs((((1 / math.sqrt(1 - pi * f[i] / 3) - 1) / (3 * ti[i])) * sf[i]) if f[i] < 0.85 else (1 / (pi ** 2 * ti[i] * sum(ar[i:]) * sum(ar[i+1:]))) * sf[i]) for i in range(n)]
+    dr2 = dtr2 / ti
+    sdr2 = np.array([math.sqrt((1 / ti[i]) ** 2 * sdtr2[i] ** 2 + dtr2[i] ** 2 / ti[i] ** 4 * sti[i] ** 2) for i in range(n)])
 
-    return dr2, np.log(dr2)
+    xlogd = logdr2 = np.log(dr2) if ln else np.log10(dr2)
+    wt = sxlogd = np.abs(sdr2 / dr2) if ln else np.abs(sdr2 / dr2) / np.log(10)
+    return dr2, xlogd, wt
 
 
-def errcal(f, ti, a39, sig39):
+def errcal(f, ti, ar, sar):
 
     # ns = 200
     # r = 1.987E-3
@@ -4681,9 +4784,9 @@ def errcal(f, ti, a39, sig39):
     sigt0 = 90.
 
     ni = len(f)
-    sumat = sum(a39)
-    sigsm = [i / sumat for i in sig39]
-    siga = [sig39[i] / a39[i] for i in range(ni)]
+    sumat = sum(ar)
+    sigsm = [i / sumat for i in sar]
+    siga = [sar[i] / ar[i] for i in range(ni)]
 
     an1 = math.pi ** 2
     sigat = 0.
@@ -4721,25 +4824,83 @@ def errcal(f, ti, a39, sig39):
 
     print(f"lovera {wt = }")
 
+    return wt
 
-    ## 下面是我重新改写 计算的  与lovera的结果接近但不一致
 
-    # a39 = np.insert(a39, 0, 0)
-    # sig39 = np.insert(sig39, 0, 0)
-    #
-    # wt = []
-    # for i in range(0, ni):
-    #
-    #     if f[i + 1] <= 0.5:
-    #         sigt = (sigt0 / ti[i]) ** 2
-    #         fp = (f[i + 1] + f[i])
-    #         a = sig39[i + 1] / a39[i + 1]
-    #         wt.append(ee * (sigt + 4 * (a ** 2 - 2 * a / a39.sum() + sigat) / (a39.sum() * fp) ** 2) ** 0.5)
-    #     else:
-    #         sigt = (sigt0 / ti[i]) ** 2
-    #         sigf = (a39[i + 1] ** 2 / a39[i + 2:].sum() ** 2 * sig39[i + 2:].sum() ** 2 + sig39[i + 1] ** 2) / a39[i + 1:].sum() ** 2
-    #         wt.append(ee * (sigt + (1 / math.log((1 - f[i + 1]) / (1 - f[i]))) ** 2 * sigf) ** 0.5)
-    #
-    # print(f"new function {wt = }")
+def geometric_model(geo: str = "sphere"):
+    """
+
+    Parameters
+    ----------
+    geo: str, sphere | cylinder | plane | cube
+    b
+
+    Returns
+    -------
+
+    """
+    if geo.lower()[:3] == 'sphere'[:3]:
+        return sphere
+    if geo.lower()[:3] == 'plane'[:3]:
+        return plane
+
+
+def sphere(bp=0.85):
+    """
+    Parameters
+    ----------
+    bp: float, breakpoint
+
+    Returns
+    -------
+
+    """
+    pi = math.pi
+    pi = 3.141592654
+
+    def func(dtr2):
+        f = 1 - (6 / pi ** 2) * math.exp(-1 * pi ** 2 * dtr2)
+        f2 = (6 / pi ** 1.5) * (pi ** 2 * dtr2) ** 0.5 - (3 / pi ** 2) * (pi ** 2 * dtr2)
+        return f if bp <= f <= 1 else f2 if 0 <= f2 else np.nan
+
+    def inv_func(f):
+        if 0 <= f < bp:
+            dtr2 = (1 - math.sqrt(1 - pi * f / 3)) ** 2 / pi
+        elif f < 1:
+            dtr2 = - math.log((1 - f) * pi ** 2 / 6) / pi ** 2
+        else:
+            dtr2 = np.nan
+        return dtr2
+
+    return func, inv_func
+
+
+def plane(bp=0.6):
+    """
+    Parameters
+    ----------
+    bp: float, breakpoint
+
+    Returns
+    -------
+
+    """
+    pi = math.pi
+    pi = 3.141592654
+
+    def func(dtr2):
+        f = 1 - (8 / pi ** 2) * math.exp(- pi ** 2 * dtr2 / 4)
+        f2 = 2 * math.sqrt(dtr2 / pi)
+        return f if bp <= f <= 1 else f2 if 0 <= f2 else np.nan
+
+    def inv_func(f):
+        if 0 <= f < bp:
+            dtr2 = pi * f ** 2 / 4
+        elif f < 1:
+            dtr2 = 4 * math.log((1 - f) * pi ** 2 / 8) / (- pi ** 2)
+        else:
+            dtr2 = np.nan
+        return dtr2
+
+    return func, inv_func
 
-    return wt